Spatially resolved transcriptome profiling in model plant species

Abstract

Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.

Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors

“…Three tissue sections were collected from each of the ten patients (A-J) diagnosed with HER2+ breast cancer included in this study (Supplementary Table 1). The collected sections were then subjected to Spatial Transcriptomics 22,23,27,28 using circular spatial spots with a diameter of 100µm. Each tumor was carefully examined by a trained pathologist, who annotated the different morphological regions in each tissue section.…”

Time-resolved transcriptome of barley anthers and meiocytes reveals robust and largely stable gene expression changes at meiosis entry

“…Sequencing of sRNA and DNA methylation in anther and meiocyte at pre-meiosis to leptotene–zygotene stages with the strongest transcriptomic changes will enhance the full picture of these interconnecting gene regulation mechanisms. Newly developed technologies, like single-cell RNA-seq (Denyer et al , 2019) and spatial transcriptomics (Giacomello et al , 2017), will increase the resolution of anther and meiocyte transcriptomes even at sub-cellular level. Nascent transcript sequencing by NET-seq (Churchman and Weissman, 2011), GRO-seq (Hetzel et al , 2016) or Neu-seq (Szabo et al , 2020) and ribosome profiling by RiboTag-seq (Lesiak et al , 2015), for example, could be used to directly evaluate transcriptional and translational activities throughout anther and meiocyte development.…”

Spatial accumulation of salicylic acid is regulated by RBOHD in potato immunity against viruses

“…Pathogen-infected leaf tissue comprises a heterogeneous mixture of host cells in different stages of defense response due to pathogen and defense signal movement from the primary infected cell (Maule et al, 2002). Recently, spatially-resolved transcriptome profiling in plant tissues has gained importance in unravelling complex regulatory networks (Giacomello et al, 2017;Shulse et al, 2019).…”